Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains

Abstract

Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming, Gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) a phylogenetic position that is distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9(T) contains 1,720 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small subunit rRNA (16S) locus.

Keywords: Chloroflexi; contamination; groundwater; hydrogen utilization; reductive dechlorination; strictly anaerobic.

Figure 1

Phylogenetic tree showing the position of D. lykanthroporepellens BL-DC-9^T relative to other strains within the phylum Chloroflexi. The tree was inferred from 1,214 aligned nucleotide positions of the 16S rRNA gene sequence using the Neighbor-Joining method within the MEGA v4.0.2 package [8]. Truepera radiovictrix RQ-24^T is shown as an outgroup and was used to root the tree. Scale bar represents 2 substitutions per 100 nucleotide positions. Numbers at branching points denote support values from 1,000 bootstrap replicates if larger than 70%. Lineages with genome sequencing projects registered in GOLD [9] are shown in blue, published genomes in bold: “Dehalococcoides” GT (CP001924), “Dehalococcoides” BAV1 (CP000688), “Dehalococcoides” CBDB1 (AJ965256), “Dehalococcoides ethenogenes” 195 (CP000027), “Dehalococcoides” VS (CP001827), Dehalogenimonas lykanthroporepellens BL-DC-9^T (CP002084), Caldilinea aerophila STL-6-O1^T (AP012337), Anaerolinea thermophila UNI-1^T (AP012029), “Thermobaculum terrenum” YNP1 (CP001825), Sphaerobacter thermophilus DSM 20745^T (CP001823), Thermomicrobium roseum DSM 5159^T (CP001275), Herpetosiphon aurantiacus DSM 785^T (CP000875), Roseiflexus castenholzii DSM 13941^T (CP000804), Chloroflexus aurantiacus J-10-fl^T (CP000909), and Chloroflexus aggregans MD-66^T (CP001337).

Figure 2

Scanning electron micrograph of cells of D. lykanthroporepellens strain BL-DC-9^T

Figure 3

Graphical circular map of the chromosome of D. lykanthroporepellens strain BL-DC-9^T. From outside to the center: Genes on the forward strand (color by COG categories), Genes on the reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content (peaks outside the circle indicate above average and peaks inside the circle indicate below average GC content), GC skew [calculated as (G − C) / (G + C); purple indicates values less than 1 and olive indicates values greater than 1]. Numbers outside the map denote nucleotide positions within the chromosome.